How to provide global coordinate system after crop volume segment?

[lassoan (Andras Lasso)]

This looks like RAS/LPS mismatch. See solution in this post:

DICOM and VTK file orientation Issue

Most common issue is LPS/RAS coordinate system mismatch. So, may try to convert your data from LPS to RAS coordinate system by transforming it using Transforms module by a matrix that has [-1,-1,1,1] in the diagonal: [image]